Topoisomerase

From Proteopedia

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Template:STRUCTURE 2h7f

Topoisomerase (TOP) winds and unwinds DNA double helix in order to enable DNA replication.

• TOPI cuts one strand of the double helix. It has 3 subclasses: TOPIA which shares its mechanism with TOPII and TOPIB which uses rotary mechanism and includes topo I and topo III. TOPIC called TOPV shares its mechanism with TOPIB but is structurally unique.
  
• TOPII cuts both strands of the double helix. Its subclasses are TOPIIA including topo II and TOPIIB which includes topo VI.
  
• TOPIV is a type of TOPII, contains an ATP-binding domain ParE and a catalytic domain ParC.
  

See also Variola Topoisomerase 1B.

Contents 1 Function 2 GO Annotations 3 3D Structures of Topoisomerase 3.1 TOPI (ATP-independent) 3.2 TOPI (ATP-dependent) – reverse gyrase 3.3 TOPIIA 3.4 TOPIIB topo VI 3.5 TOPIII 3.6 TOPIV 3.7 TOPV

Function

The reaction catalyzed by topoisomerases leads to the conversion of one topological isomer of DNA to another. TOP3 is a potent decatenase.

GO Annotations

Database	ID	Symbol	Qualifier	GO Identifier	GO Term Name	Aspect	Evidence	Reference	With	Taxon	Date	Assigned by	Product Form ID
UniProtKB	P14294	topB		GO:0006259	DNA metabolic process	P	IEA	InterPro2GO	InterPro:IPR006154	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0006265	DNA topological change	P	IEA	InterPro2GO	InterPro:IPR000380	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0006265	DNA topological change	P	IEA	InterPro2GO	InterPro:IPR003601	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0006265	DNA topological change	P	IEA	InterPro2GO	InterPro:IPR003602	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0006265	DNA topological change	P	IEA	InterPro2GO	InterPro:IPR005738	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0006265	DNA topological change	P	IEA	InterPro2GO	InterPro:IPR013497	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0006265	DNA topological change	P	IEA	InterPro2GO	InterPro:IPR013824	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0006265	DNA topological change	P	IEA	InterPro2GO	InterPro:IPR013825	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0006268	DNA unwinding involved in replication	P	IEA	InterPro2GO	InterPro:IPR013824	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0006268	DNA unwinding involved in replication	P	IEA	InterPro2GO	InterPro:IPR013825	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0000166	nucleotide binding	F	IEA	Swiss-Prot Keywords2GO	SP_KW:KW-0547	83333	20101127	UniProtKB
UniProtKB	P14294	topB		GO:0003676	nucleic acid binding	F	IEA	InterPro2GO	InterPro:IPR006154	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0003677	DNA binding	F	IEA	InterPro2GO	InterPro:IPR000380	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0003677	DNA binding	F	IEA	InterPro2GO	InterPro:IPR003601	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0003677	DNA binding	F	IEA	InterPro2GO	InterPro:IPR003602	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0003677	DNA binding	F	IEA	InterPro2GO	InterPro:IPR005738	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0003677	DNA binding	F	IEA	InterPro2GO	InterPro:IPR013497	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0003677	DNA binding	F	IEA	InterPro2GO	InterPro:IPR013824	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0003677	DNA binding	F	IEA	InterPro2GO	InterPro:IPR013825	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0003677	DNA binding	F	IEA	Swiss-Prot Keywords2GO	SP_KW:KW-0238	83333	20101127	UniProtKB
UniProtKB	P14294	topB		GO:0003916	DNA topoisomerase activity	F	IEA	InterPro2GO	InterPro:IPR003601	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0003916	DNA topoisomerase activity	F	IEA	InterPro2GO	InterPro:IPR003602	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0003916	DNA topoisomerase activity	F	IEA	InterPro2GO	InterPro:IPR005738	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0003916	DNA topoisomerase activity	F	IEA	InterPro2GO	InterPro:IPR013497	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0003916	DNA topoisomerase activity	F	IEA	InterPro2GO	InterPro:IPR013824	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0003916	DNA topoisomerase activity	F	IEA	InterPro2GO	InterPro:IPR013825	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0003916	DNA topoisomerase activity	F	IEA	Swiss-Prot Keywords2GO	SP_KW:KW-0799	83333	20101127	UniProtKB
UniProtKB	P14294	topB		GO:0003917	DNA topoisomerase type I activity	F	IDA	PMID:6326814		83333	20100621	EcoliWiki
UniProtKB	P14294	topB		GO:0003917	DNA topoisomerase type I activity	F	IEA	InterPro2GO	InterPro:IPR000380	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0003917	DNA topoisomerase type I activity	F	IEA	EC2GO	EC:5.99.1.2	83333	20100703	UniProtKB
UniProtKB	P14294	topB		GO:0005515	protein binding	F	IPI	PMID:15690043	frlR (FRLR_ECOLI)	83333	20101127	IntAct
UniProtKB	P14294	topB		GO:0005524	ATP binding	F	IEA	Swiss-Prot Keywords2GO	SP_KW:KW-0067	83333	20101127	UniProtKB
UniProtKB	P14294	topB		GO:0016853	isomerase activity	F	IEA	Swiss-Prot Keywords2GO	SP_KW:KW-0413	83333	20101127	UniProtKB
UniProtKB	P14294	topB		GO:0005694	chromosome	C	IEA	InterPro2GO	InterPro:IPR000380	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0005694	chromosome	C	IEA	InterPro2GO	InterPro:IPR003601	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0005694	chromosome	C	IEA	InterPro2GO	InterPro:IPR003602	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0005694	chromosome	C	IEA	InterPro2GO	InterPro:IPR005738	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0005694	chromosome	C	IEA	InterPro2GO	InterPro:IPR013497	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0005694	chromosome	C	IEA	InterPro2GO	InterPro:IPR013824	83333	20101127	InterPro
UniProtKB	P14294	topB		GO:0005694	chromosome	C	IEA	InterPro2GO	InterPro:IPR013825	83333	20101127	InterPro

Copied from [1] Last updated Dec 2 2010

3D Structures of Topoisomerase

Updated on 21-August-2014

TOPI (ATP-independent)

3igc, 2h7f, 2h7g – TOPI+DNA – Smallpox virus
2gai, 2gaj – TOPI – Thermotoga maritime
2f4q – TOPIB – Deinococcus radiodurans
1tl8, 1sc7 – hTOPI+DNA+indenoisoquinoline – human
1seu - hTOPI+DNA+indolocarbazole
1t8i, 1rr8, 1rrj - hTOPI+DNA+camptothesin
1r49 – hTOPI (mutant)
1mw8 – hTOPI (mutant) N-terminal+DNA
1mw9 - hTOPI (mutant) N-terminal
1nh3 – hTOPI C-terminal+DNA+Ara-C
1k4s, 1lpq, 1ej9, 1a31, 1a35, 1a36 – hTOPI+DNA
1k4t - hTOPI+DNA+topotecan
1cy0 – EcTOPI+DNA - Escherichia coli
3px7 – EcTOPI (mutant) +DNA
1cy2, 1cy1 – EcTOPI+5’TPTPTP3’
1cy6, 1cy7, 1cy8 – EcIOPI+TMP
1cy9, 1cyy – EcTOPI domain II+III
1yua – EcTOPI C-terminal
1ecl, 1cy4 - EcTOPI N-terminal
3pwt - EcTOPIA N-terminal (mutant)
1a41 – VvTOPI C-terminal – Vaccinia virus
1vcc – VvTOPI N-terminal
1ois – yTOPI N-terminal - yeast

TOPI (ATP-dependent) – reverse gyrase

4ddt, 4ddu, 4ddv, 4ddw, 4ddx – TmTOPI

TOPIIA

3l4j – yTOPII apo+DNA
3l4k - yTOPII+DNA+Zn
2rgr - yTOPIIA+DNA
4gfh - yTOPIIA+DNA + ANPPNP
1qzr – yTOPII N-terminal+dexrazoxane
1pvg – yTOPII N-terminal
1bjt, 1bgw – yTOPII core
3ksa, 2ksb – SpTOPIIA+DNA – Streptococcus pneumoniae
1zxm – hTOPIIA+AMP-PNP
1zxn - hTOPIIA+ADP
4fm9 - hTOPIIA+DNA
3kua – TOPII residues 362-493 + CCDB – Vibrio fischeri

TOPIIB topo VI

2zbk – SsTOPIIB subunit A+B – Sulfolobus shibatae
2hkj, 1mu5, 1mx0 - SsTOPIIB subunit B
1z59, 1z5a - SsTOPIIB subunit B+ADP
1z5b - SsTOPIIB subunit B+ADP+AlF4
1z5c - SsTOPIIB subunit B+ADP+Pi
2q2e - TOPIIB subunit A+B – Methanosarcina mazei
1d3y - TOPIIB subunit A - Methanocaldococcus janaschii
4j3n - hTOPIIB subunit A+B + DNA
4g0w, 3qx3, 4g0v, 4g0u - hTOPIIB + DNA + anti-cancer drug

TOPIII

2o19, 2o54, 2o59, 2o5c, 2o5e, 1i7d – EcTOPIII+DNA
1d6m - EcTOPIII
4cgy, 4cht – hTOPIIIα + RecQ-mediated genome instability protein

TOPIV

3fv5 – EcTOPIV subunit B
4hz0 - EcTOPIV subunit B + inhibitor
1zvt, 1zvu - EcTOPIV subunit A
4mn4 - EcTOPIV subunit A + MukB
1s14 – EcTOPIV ParE
1s16 - EcTOPIV ParE+ADPNP
3ltn, 3k9f, 3ksb, 3rad, 3rae, 3raf, 4i3h, 4juo - SpTOPIV subunit A+B+DNA
3foe, 3fof - SpTOPIV subunit A+B+DNA+quinolone
2nov - SpTOPIV subunit A
4em7, 4emv, 4lp0, 4lpb, 4mb9, 4mbc, 4mot - SpTOPIV subunit B + inhibitor
2inr - TOPIV subunit A – Staphylococcus aureus
1wp5 – TOPIV C-terminal – Geobacillus stearothermophilus
2xkj – AbTOPIV pare+parc subunits – Acinetobacter baumannii
2xkk - AbTOPIV pare+parc subunits+DNA
3lnu, 3lps - TOPIV subunit B N-terminal – Xanthomonas oryzae
4hxz, 4hy1 - hTOPIV subunit B + inhibitor
4hym, 4kqv - TOPIV subunit B + inhibitor – Francisella tularensis
4hz5 - TOPIV subunit B + inhibitor – Enterococcus faecalis

TOPV

2csb, 2csd, 4gfj – TOPV – Methanopyrus kandleri
3m6k, 3m7g – MkTOPV N-terminal
3m6z - MkTOPV N-terminal+guanidine
3m7d - MkTOPV N-terminal+dioxane
Created with the participation of Sonny Zhao.